hygine
commented
4 years ago $cat /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/corrected/configs/config.info
; = HAMMER =
; input options: working dir, input files, offset, and possibly kmers
dataset /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/input_dataset.yaml
input_working_dir /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/tmp/hammer_V6Mn1L
input_trim_quality 4
input_qvoffset
output_dir /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/corrected
; == HAMMER GENERAL == ; general options general_do_everything_after_first_iteration 1 general_hard_memory_limit 125 general_max_nthreads 16 general_tau 1 general_max_iterations 1 general_debug 0
; count k-mers count_do 1 count_numfiles 16 count_merge_nthreads 16 count_split_buffer 0 count_filter_singletons 0
; hamming graph clustering hamming_do 1 hamming_blocksize_quadratic_threshold 50
; bayesian subclustering bayes_do 1 bayes_nthreads 16 bayes_singleton_threshold 0.995 bayes_nonsingleton_threshold 0.9 bayes_use_hamming_dist 0 bayes_discard_only_singletons 0 bayes_debug_output 0 bayes_hammer_mode 0 bayes_write_solid_kmers 0 bayes_write_bad_kmers 0 bayes_initial_refine 1
; iterative expansion step expand_do 1 expand_max_iterations 25 expand_nthreads 16 expand_write_each_iteration 0 expand_write_kmers_result 0
; read correction correct_do 1 correct_discard_bad 0 correct_use_threshold 1 correct_threshold 0.98 correct_nthreads 16 correct_readbuffer 100000 correct_stats 1
asl
组装 + 16S预测 + 16S blast
2020-03-18 12:57:01: sh /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/work_sh/assembly.sh && touch /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/work_sh/assembly.sh.done
== Warning == No assembly mode was sepcified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.
Command line: /share/nas1/linhj/bin/software/SPAdes-3.14.0-Linux/bin//spades.py -k 21,33,55,77,99 --careful --pe1-1 /share/nas1/linhj/bin/pollution_check/R01_test/R01/Bacteria_X972-01-R01_good_1.fq --pe1-2 /share/nas1/linhj/bin/pollution_check/R01_test/R01/Bacteria_X972-01-R01_good_2.fq -o /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly
System information: SPAdes version: 3.14.0 Python version: 2.7.8 OS: Linux-2.6.32-431.11.2.el6.x86_64-x86_64-with-centos-6.5-Final
Output dir: /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly Mode: read error correction and assembling Debug mode is turned OFF
Dataset parameters: Standard mode For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/share/nas1/linhj/bin/pollution_check/R01_test/R01/Bacteria_X972-01-R01_good_1.fq'] right reads: ['/share/nas1/linhj/bin/pollution_check/R01_test/R01/Bacteria_X972-01-R01_good_2.fq'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 33, 55, 77, 99] Repeat resolution is enabled Mismatch careful mode is turned ON MismatchCorrector will be used Coverage cutoff is turned OFF Other parameters: Dir for temp files: /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/tmp Threads: 16 Memory limit (in Gb): 125
======= SPAdes pipeline started. Log can be found here: /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/spades.log
/share/nas1/linhj/bin/pollution_check/R01_test/R01/Bacteria_X972-01-R01_good_2.fq: max reads length: 150 /share/nas1/linhj/bin/pollution_check/R01_test/R01/Bacteria_X972-01-R01_good_1.fq: max reads length: 150
Reads length: 150
===== Read error correction started.
===== Read error correction started.
== Running: /share/nas1/linhj/bin/software/SPAdes-3.14.0-Linux/bin/spades-hammer /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/corrected/configs/config.info
0:00:00.079 8M / 11M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.14.0, git revision c831f9be30a4364383cd4ebe5b78cdfcaad1acc9 0:00:00.687 8M / 11M INFO General (main.cpp : 76) Loading config from /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/corrected/configs/config.info 0:00:00.967 8M / 12M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.967 8M / 12M INFO General (memory_limit.cpp : 49) Memory limit set to 125 Gb 0:00:00.967 8M / 12M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:01.271 8M / 12M ERROR General (main.cpp : 89) Failed to determine offset! Specify it manually and restart, please!
== Error == system call for: "['/share/nas1/linhj/bin/software/SPAdes-3.14.0-Linux/bin/spades-hammer', '/share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/corrected/configs/config.info']" finished abnormally, OS return value: 255
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory.
SPAdes log can be found here: /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/assembly/spades.log
Thank you for using SPAdes! 2020-03-18 12:57:09: Error: command fail: sh /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/work_sh/assembly.sh && touch /share/nas1/linhj/bin/pollution_check/R01_test/new_test2_R01/work_sh/assembly.sh.done 2020-03-18 12:57:09: Elaseped time: 8s